Alignments for a candidate for ilvD in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methanosarcina mazei Go1

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011032213.1 MM_RS01430 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000007065.1:WP_011032213.1
          Length = 553

 Score =  660 bits (1704), Expect = 0.0
 Identities = 321/553 (58%), Positives = 424/553 (76%), Gaps = 6/553 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+S  IK G +RA +RSLL   G+TD + ++PFI + NS+ DI+PGHIHL +LAEAVK G
Sbjct: 1   MRSAIIKEGPERAANRSLLKATGVTDAEMKRPFIAVVNSWNDIIPGHIHLNKLAEAVKAG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +  AGGV FEF+T+ +CDGIAM H+GMKYSL SRE++ DT+E M  AH  DG+VL+PTCD
Sbjct: 61  IRNAGGVPFEFHTIGVCDGIAMGHEGMKYSLPSREVIEDTIELMVRAHQFDGMVLIPTCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPG LMAA RLDIPAIVVTGGPMLPG    +  DLI+V+EGVG   AG++SE ELE L
Sbjct: 121 KIVPGHLMAAGRLDIPAIVVTGGPMLPGYVDDKYTDLISVFEGVGAFRAGKLSEAELERL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           E  +C G  SCAG+FTANTMAC+TEALG+SLPGCATAHAV ++K +IA+ SG+RIVE+V+
Sbjct: 181 ENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHAVDAKKVRIAKESGERIVELVK 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           +N+ P  I++ ++FENA+MVD+A+GGSTNTTLH+PA+A E  GL + L+ FDELSR  PH
Sbjct: 241 QNITPRKIVTYKSFENAIMVDMAVGGSTNTTLHLPALAHEF-GLELPLEAFDELSRKTPH 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKV----GHR 356
           + S+ P G + ML  DRAGG+ AV++ L   ++ + +T  G+T+ ENI  +++     + 
Sbjct: 300 LISLRPGGPNFMLHFDRAGGVEAVMQRLSSKLHLDQLTVNGKTIGENISELEIINPKLNE 359

Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416
           ++I+ L++P+H+EGG+A+L+G+LAP GSVVKQ AV   M VH GPAKV++ E++ M++I 
Sbjct: 360 EIIKTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMRVHTGPAKVYDCEEDAMKSIL 419

Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMG-LERVALITDGRFSGGTRGPCVG 475
            G +  GD++VIRYEGPKGGPGMREML  T+AIAGMG LE VAL+TDGRFSGGTRGPC+G
Sbjct: 420 AGEVKPGDIVVIRYEGPKGGPGMREMLAATAAIAGMGLLESVALVTDGRFSGGTRGPCIG 479

Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARY 535
           HVSPEA E GP+  V DGD+I I+IP R L + +S  E+E+R      P + V G+LARY
Sbjct: 480 HVSPEASEGGPIGLVKDGDLIEINIPERILNLKVSEEELEKRRSVFNPPEKKVTGYLARY 539

Query: 536 RKLAGSADTGAVL 548
           ++   SA+TG ++
Sbjct: 540 QRAVHSANTGGIV 552


Lambda     K      H
   0.319    0.136    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1080
Number of extensions: 59
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 549
Length of database: 553
Length adjustment: 36
Effective length of query: 513
Effective length of database: 517
Effective search space:   265221
Effective search space used:   265221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_011032213.1 MM_RS01430 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.15756.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-247  806.8   3.6     5e-247  806.7   3.6    1.0  1  lcl|NCBI__GCF_000007065.1:WP_011032213.1  MM_RS01430 dihydroxy-acid dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007065.1:WP_011032213.1  MM_RS01430 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  806.7   3.6    5e-247    5e-247       1     542 [.      14     553 .]      14     553 .] 0.99

  Alignments for each domain:
  == domain 1  score: 806.7 bits;  conditional E-value: 5e-247
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               a+r+llkatG++d+++++P+iavvns+++i+Pgh+hl++la++vk++i++aGgv++ef ti+v+DGiam
  lcl|NCBI__GCF_000007065.1:WP_011032213.1  14 ANRSLLKATGVTDAEMKRPFIAVVNSWNDIIPGHIHLNKLAEAVKAGIRNAGGVPFEFHTIGVCDGIAM 82 
                                               68******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGmkysLpsre+i D++e +v+ah++D++v+i++CDkivPG lmaa rl+iPaivv+GGpm +g + 
  lcl|NCBI__GCF_000007065.1:WP_011032213.1  83 GHEGMKYSLPSREVIEDTIELMVRAHQFDGMVLIPTCDKIVPGHLMAAGRLDIPAIVVTGGPMLPGYVD 151
                                               ********************************************************************9 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 +  dl++vfe+vg+  agklse+ele++e+ +c +agsC+G+ftan+mac+tealGlslPg++t++a
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 152 -DKYTDLISVFEGVGAFRAGKLSEAELERLENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHA 219
                                               .7999**************************************************************** PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               ++a+k ++ak+sg+rivelvk+ni+Pr+i+t ++fenai++d+a+GGstnt+Lhl+a+a+e g++l l+
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 220 VDAKKVRIAKESGERIVELVKQNITPRKIVTYKSFENAIMVDMAVGGSTNTTLHLPALAHEFGLELPLE 288
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344
                                                fd+lsrk+P+l +l+P+g +++   +raGGv+av++ l  + +lh d ltv Gkt++e++++ ++++ 
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 289 AFDELSRKTPHLISLRPGGPNFMLHFDRAGGVEAVMQRL--SSKLHLDQLTVNGKTIGENISELEIINp 355
                                               ***************************************..899********************99865 PP

                                 TIGR00110 345 .vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvk 412
                                                +++++i++l+np+++egg+avLkG+la++G+vvk+a+v+ ++ +++Gpakv++ ee+a+++il+g+vk
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 356 kLNEEIIKTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMRVHTGPAKVYDCEEDAMKSILAGEVK 424
                                               58899**************************************************************** PP

                                 TIGR00110 413 eGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaial 481
                                                Gd+vviryeGPkGgPGmremLa t+a++g+GL ++vaL+tDGrfsGgtrG++iGhvsPea egG+i+l
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 425 PGDIVVIRYEGPKGGPGMREMLAATAAIAGMGLLESVALVTDGRFSGGTRGPCIGHVSPEASEGGPIGL 493
                                               ********************************************************************* PP

                                 TIGR00110 482 vedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               v+dGD i+i+i++r l+l+vseeel++rr   +++e ++v g+La+y++ v sa++G+++d
  lcl|NCBI__GCF_000007065.1:WP_011032213.1 494 VKDGDLIEINIPERILNLKVSEEELEKRRSVFNPPE-KKVTGYLARYQRAVHSANTGGIVD 553
                                               *****************************9999999.88******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (553 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.66
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis